library(plotly)
library(plyr)
library(dplyr)
library(readxl)
parse_sheet <- function(excel_sheet, excel_file) {
df <- readxl::read_excel(excel_file, sheet = excel_sheet)
df <- df[, c('...1', 'dist mean', 'significant')]
df['source'] <- excel_sheet
colnames(df) <- c('target', 'value', 'significant', 'source')
return (df)
}
cat_file <- '../CAT/fung-vs-li/vitro_vivo_euclidean.xlsx'
sheets <- excel_sheets(cat_file)[-1]
dfs <- lapply(sheets, parse_sheet, excel_file=cat_file)
dfs <- do.call("rbind", dfs)
labels <- unique(c(dfs$target, dfs$source))
dfs$source_num <- match(dfs$source, labels) -1
dfs$target_num <- match(dfs$target, labels) -1
dfs$color <- mapvalues(dfs$significant, from=c(TRUE, FALSE), to=c("#4c92c3","#cccccc"))
dfs$updated_value <- abs(dfs$value - max(dfs$value))
plot_ly(
type = "sankey",
orientation = "h",
node = list(
label = labels,
pad = 15,
thickness = 20,
line = list(
color = "black",
width = 0.5
)
),
link = list(
source = dfs$source_num,
target = dfs$target_num,
color = dfs$color,
value = dfs$value
)
) %>%
layout(
title = "Vitro vs Li et al., 2020",
font = list(
size = 20
)
)
Session info
devtools::session_info()
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.2 (2021-11-01)
## os macOS Big Sur 10.16
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Copenhagen
## date 2022-01-24
## pandoc 2.17.0.1 @ /usr/local/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## bslib 0.3.1 2021-10-06 [1] CRAN (R 4.1.0)
## cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.0)
## callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0)
## cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.1.0)
## cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.0)
## colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.1.0)
## crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.0)
## crosstalk 1.2.0 2021-11-04 [1] CRAN (R 4.1.0)
## data.table 1.14.2 2021-09-27 [1] CRAN (R 4.1.0)
## desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.0)
## devtools 2.4.3 2021-11-30 [1] CRAN (R 4.1.0)
## digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.0)
## dplyr * 1.0.7 2021-06-18 [1] CRAN (R 4.1.0)
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
## evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0)
## fansi 1.0.2 2022-01-14 [1] CRAN (R 4.1.2)
## fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0)
## fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.0)
## generics 0.1.1 2021-10-25 [1] CRAN (R 4.1.0)
## ggplot2 * 3.3.5 2021-06-25 [1] CRAN (R 4.1.0)
## glue 1.6.0 2021-12-17 [1] CRAN (R 4.1.0)
## gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
## htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.0)
## htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.1.0)
## httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.0)
## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.1.0)
## jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.1.0)
## knitr 1.37 2021-12-16 [1] CRAN (R 4.1.0)
## lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0)
## lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.0)
## magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0)
## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.0)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
## pillar 1.6.4 2021-10-18 [1] CRAN (R 4.1.0)
## pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.1.0)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
## pkgload 1.2.4 2021-11-30 [1] CRAN (R 4.1.0)
## plotly * 4.10.0 2021-10-09 [1] CRAN (R 4.1.0)
## plyr * 1.8.6 2020-03-03 [1] CRAN (R 4.1.0)
## prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
## processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.0)
## ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.0)
## purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
## R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0)
## Rcpp 1.0.8 2022-01-13 [1] CRAN (R 4.1.2)
## readxl * 1.3.1 2019-03-13 [1] CRAN (R 4.1.0)
## remotes 2.4.2 2021-11-30 [1] CRAN (R 4.1.0)
## rlang 0.4.12 2021-10-18 [1] CRAN (R 4.1.0)
## rmarkdown 2.11 2021-09-14 [1] CRAN (R 4.1.2)
## rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.0)
## rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
## sass 0.4.0 2021-05-12 [1] CRAN (R 4.1.0)
## scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.0)
## sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.0)
## stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.0)
## stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
## testthat 3.1.1 2021-12-03 [1] CRAN (R 4.1.0)
## tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.0)
## tidyr 1.1.4 2021-09-27 [1] CRAN (R 4.1.0)
## tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.0)
## usethis 2.1.5 2021-12-09 [1] CRAN (R 4.1.0)
## utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0)
## vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0)
## viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.1.0)
## withr 2.4.3 2021-11-30 [1] CRAN (R 4.1.0)
## xfun 0.29 2021-12-14 [1] CRAN (R 4.1.0)
## yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0)
##
## [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
##
## ──────────────────────────────────────────────────────────────────────────────